def add_sweeps(self, items):
items_with_sweeps = []
for item in items:
items_with_sweeps.append(item)
if not item.is_blank():
items_with_sweeps.append(RunSample.create_sweep(self.run))
return items_with_sweeps
def add_sweeps(self, items):
items_with_sweeps = []
for item in items:
items_with_sweeps.append(item)
if not item.is_blank():
items_with_sweeps.append(RunSample.create_sweep(self.run))
return items_with_sweeps
def apply_method_rules(self, sample_block):
number_of_methods = self.run.number_of_methods or 1
if number_of_methods <= 1:
return sample_block
for sample in sample_block:
sample.method_number = 1
sample.save()
extended_sample_block = []
if self.run.is_method_type_individual_vial():
extended_sample_block = sample_block[:]
for method_number in range(2, number_of_methods+1):
for sample in sample_block:
extended_sample_block.append(RunSample.create_copy(sample, method_number))
else:
for sample in sample_block:
extended_sample_block.append(sample)
for method_number in range(2, number_of_methods+1):
extended_sample_block.append(RunSample.create_copy(sample, method_number))
return extended_sample_block
def forwards(self, orm):
"Sanitize filenames for the incomplete samples of incomplete runs."
incomplete = orm.RunSample.objects.filter(complete=False).exclude(run__state=RUN_STATES.COMPLETE[0])
checked = 0
changed = 0
for sample in incomplete:
old = sample.filename
sample.filename = RunSample.sanitize_filename(old)
if old != sample.filename:
sample.save()
changed += 1
checked += 1
print "Checked filenames of %d samples, changed %d." % (checked, changed)
def create_insertion_map(self, samples, rules):
'''Returns a dict: keys are positions in the sample_list, values an array of items to insert at that position'''
insertion_map = {}
for rule in rules:
sample_count = rule.sample_count
start_idxs = range(0, len(samples), sample_count)
end_idxs = range(sample_count, len(samples), sample_count) + [len(samples)]
for start,end in zip(start_idxs, end_idxs):
position = end
if rule.in_random_position:
position = random.randint(start+1, end)
arr = insertion_map.setdefault(position, [])
for i in range(rule.count):
arr.append(RunSample.create(self.run, rule.component))
return insertion_map
def apply_method_rules(self, sample_block):
number_of_methods = self.run.number_of_methods or 1
if number_of_methods <= 1:
return sample_block
for sample in sample_block:
sample.method_number = 1
sample.save()
extended_sample_block = []
if self.run.is_method_type_individual_vial():
extended_sample_block = sample_block[:]
for method_number in range(2, number_of_methods + 1):
for sample in sample_block:
extended_sample_block.append(
RunSample.create_copy(sample, method_number))
else:
for sample in sample_block:
extended_sample_block.append(sample)
for method_number in range(2, number_of_methods + 1):
extended_sample_block.append(
RunSample.create_copy(sample, method_number))
return extended_sample_block
def create_insertion_map(self, samples, rules):
'''Returns a dict: keys are positions in the sample_list, values an array of items to insert at that position'''
insertion_map = {}
for rule in rules:
sample_count = rule.sample_count
start_idxs = range(0, len(samples), sample_count)
end_idxs = range(sample_count, len(samples),
sample_count) + [len(samples)]
for start, end in zip(start_idxs, end_idxs):
position = end
if rule.in_random_position:
position = random.randint(start + 1, end)
arr = insertion_map.setdefault(position, [])
for i in range(rule.count):
arr.append(RunSample.create(self.run, rule.component))
return insertion_map
def create_end_block(self):
end_block = []
for rule in self.run.rule_generator.end_block_rules:
for i in range(rule.count):
end_block.append(RunSample.create(self.run, rule.component))
return end_block
def create_end_block(self):
end_block = []
for rule in self.run.rule_generator.end_block_rules:
for i in range(rule.count):
end_block.append(RunSample.create(self.run, rule.component))
return end_block
